Starting phenix.real_space_refine (version: dev) on Thu Dec 15 19:18:39 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syu_25541/12_2022/7syu_25541.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syu_25541/12_2022/7syu_25541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syu_25541/12_2022/7syu_25541.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syu_25541/12_2022/7syu_25541.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syu_25541/12_2022/7syu_25541.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syu_25541/12_2022/7syu_25541.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B ASP 31": "OD1" <-> "OD2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 73": "OD1" <-> "OD2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B ASP 200": "OD1" <-> "OD2" Residue "C PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 254": "OD1" <-> "OD2" Residue "E ASP 14": "OD1" <-> "OD2" Residue "E PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E ASP 162": "OD1" <-> "OD2" Residue "E GLU 216": "OE1" <-> "OE2" Residue "F TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 118": "OE1" <-> "OE2" Residue "F TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 32": "OD1" <-> "OD2" Residue "G TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 195": "OE1" <-> "OE2" Residue "G GLU 197": "OE1" <-> "OE2" Residue "H ASP 19": "OD1" <-> "OD2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H GLU 43": "OE1" <-> "OE2" Residue "H GLU 44": "OE1" <-> "OE2" Residue "H TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 165": "OE1" <-> "OE2" Residue "H GLU 204": "OE1" <-> "OE2" Residue "I PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 131": "OE1" <-> "OE2" Residue "I ASP 132": "OD1" <-> "OD2" Residue "I PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 28": "OE1" <-> "OE2" Residue "J ASP 61": "OD1" <-> "OD2" Residue "J TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 163": "OE1" <-> "OE2" Residue "J PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 194": "OE1" <-> "OE2" Residue "K GLU 42": "OE1" <-> "OE2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 107": "OE1" <-> "OE2" Residue "K ASP 152": "OD1" <-> "OD2" Residue "L PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 3": "OD1" <-> "OD2" Residue "M TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 52": "OE1" <-> "OE2" Residue "M PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 35": "OE1" <-> "OE2" Residue "O GLU 103": "OE1" <-> "OE2" Residue "P PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 51": "OE1" <-> "OE2" Residue "P ASP 65": "OD1" <-> "OD2" Residue "P ASP 131": "OD1" <-> "OD2" Residue "Q PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 40": "OE1" <-> "OE2" Residue "R TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 101": "OD1" <-> "OD2" Residue "R ASP 123": "OD1" <-> "OD2" Residue "R GLU 128": "OE1" <-> "OE2" Residue "S GLU 18": "OE1" <-> "OE2" Residue "S GLU 75": "OE1" <-> "OE2" Residue "S GLU 104": "OE1" <-> "OE2" Residue "S ASP 110": "OD1" <-> "OD2" Residue "S PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 58": "OE1" <-> "OE2" Residue "T PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 38": "OE1" <-> "OE2" Residue "W ASP 66": "OD1" <-> "OD2" Residue "W PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 115": "OE1" <-> "OE2" Residue "Y TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 88": "OD1" <-> "OD2" Residue "Y GLU 95": "OE1" <-> "OE2" Residue "Y TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 77": "OD1" <-> "OD2" Residue "Z GLU 86": "OE1" <-> "OE2" Residue "b ASP 33": "OD1" <-> "OD2" Residue "b GLU 90": "OE1" <-> "OE2" Residue "b ASP 94": "OD1" <-> "OD2" Residue "b PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 36": "OD1" <-> "OD2" Residue "d ASP 37": "OD1" <-> "OD2" Residue "d GLU 64": "OE1" <-> "OE2" Residue "e TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 144": "OD1" <-> "OD2" Residue "h GLU 145": "OE1" <-> "OE2" Residue "h TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 223": "OE1" <-> "OE2" Residue "h TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 234": "OD1" <-> "OD2" Residue "h GLU 282": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 80962 Number of models: 1 Model: "" Number of chains: 38 Chain: "2" Number of atoms: 36227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1697, 36227 Classifications: {'RNA': 1697} Modifications used: {'5*END': 1, 'rna2p_pur': 143, 'rna2p_pyr': 112, 'rna3p_pur': 754, 'rna3p_pyr': 688} Link IDs: {'rna2p': 254, 'rna3p': 1442} Chain breaks: 11 Chain: "B" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1710 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "D" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1716 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "F" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "G" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1509 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "H" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "I" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1488 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 1 Chain: "J" Number of atoms: 1691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Conformer: "B" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} bond proxies already assigned to first conformer: 1709 Chain: "K" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 810 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "M" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1233 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "O" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "P" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "Q" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 997 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "R" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 135} Chain: "S" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1068 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "T" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1190 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "U" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1097 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 795 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "W" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "X" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Chain: "Y" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Z" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "a" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "b" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "c" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "d" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 530 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "e" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "f" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 457 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "g" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 555 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "h" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "n" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 239 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "z" Number of atoms: 4017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 4017 Classifications: {'RNA': 188} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 17, 'rna3p_pur': 80, 'rna3p_pyr': 74} Link IDs: {'rna2p': 34, 'rna3p': 153} Chain breaks: 1 Chain: "i" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1604 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 3, 'rna3p_pur': 32, 'rna3p_pyr': 30} Link IDs: {'rna2p': 12, 'rna3p': 62} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 69800 SG CYS b 77 94.796 129.076 134.550 1.00 63.88 S Time building chain proxies: 33.07, per 1000 atoms: 0.41 Number of scatterers: 80962 At special positions: 0 Unit cell: (236.55, 199.5, 261.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 180 16.00 P 1958 15.00 O 20529 8.00 N 14905 7.00 C 43389 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 141 " - pdb=" SG CYS g 144 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 27.49 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 201 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 77 " 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9076 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 55 sheets defined 34.1% alpha, 17.5% beta 522 base pairs and 1042 stacking pairs defined. Time for finding SS restraints: 22.17 Creating SS restraints... Processing helix chain 'B' and resid 12 through 22 removed outlier: 4.031A pdb=" N LEU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 83 through 95 Processing helix chain 'B' and resid 130 through 137 removed outlier: 4.279A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR B 135 " --> pdb=" O HIS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 187 removed outlier: 3.882A pdb=" N VAL B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 removed outlier: 3.733A pdb=" N LEU B 201 " --> pdb=" O MET B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'C' and resid 23 through 26 removed outlier: 3.697A pdb=" N SER C 26 " --> pdb=" O ASP C 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 23 through 26' Processing helix chain 'C' and resid 57 through 62 removed outlier: 3.859A pdb=" N GLY C 61 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 57 through 62' Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 157 through 175 removed outlier: 3.745A pdb=" N GLU C 175 " --> pdb=" O ILE C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 189 Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 224 through 231 removed outlier: 3.640A pdb=" N LEU C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.506A pdb=" N ARG D 68 " --> pdb=" O THR D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 84 Processing helix chain 'D' and resid 91 through 98 removed outlier: 3.666A pdb=" N ASP D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 removed outlier: 3.676A pdb=" N SER D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 217 Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 264 through 277 removed outlier: 5.559A pdb=" N ASP D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N HIS D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 29 removed outlier: 3.553A pdb=" N PHE E 11 " --> pdb=" O LYS E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.695A pdb=" N VAL E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 54 through 59' Processing helix chain 'E' and resid 63 through 78 removed outlier: 3.695A pdb=" N GLY E 78 " --> pdb=" O GLN E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 96 Processing helix chain 'E' and resid 97 through 111 removed outlier: 4.016A pdb=" N GLY E 111 " --> pdb=" O TYR E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 161 through 165 removed outlier: 3.816A pdb=" N VAL E 164 " --> pdb=" O GLY E 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 51 Processing helix chain 'F' and resid 57 through 66 removed outlier: 3.539A pdb=" N VAL F 61 " --> pdb=" O THR F 57 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS F 62 " --> pdb=" O GLY F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 119 No H-bonds generated for 'chain 'F' and resid 117 through 119' Processing helix chain 'F' and resid 247 through 263 Processing helix chain 'G' and resid 62 through 66 Processing helix chain 'G' and resid 67 through 77 removed outlier: 3.961A pdb=" N MET G 77 " --> pdb=" O THR G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 105 removed outlier: 4.031A pdb=" N THR G 89 " --> pdb=" O LYS G 85 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR G 104 " --> pdb=" O ILE G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 119 removed outlier: 3.709A pdb=" N VAL G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN G 114 " --> pdb=" O GLN G 110 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA G 115 " --> pdb=" O VAL G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 162 Processing helix chain 'G' and resid 168 through 182 removed outlier: 3.586A pdb=" N ALA G 174 " --> pdb=" O ALA G 170 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN G 179 " --> pdb=" O ASP G 175 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA G 180 " --> pdb=" O GLU G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 202 Processing helix chain 'H' and resid 24 through 28 removed outlier: 3.530A pdb=" N TYR H 28 " --> pdb=" O ARG H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 152 through 156 removed outlier: 3.683A pdb=" N GLN H 155 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 236 removed outlier: 3.552A pdb=" N LEU H 185 " --> pdb=" O THR H 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 33 Processing helix chain 'I' and resid 35 through 40 removed outlier: 4.418A pdb=" N ALA I 38 " --> pdb=" O ASP I 35 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU I 40 " --> pdb=" O LYS I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 67 No H-bonds generated for 'chain 'I' and resid 65 through 67' Processing helix chain 'I' and resid 68 through 75 removed outlier: 3.513A pdb=" N PHE I 72 " --> pdb=" O GLN I 68 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE I 75 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 87 removed outlier: 4.102A pdb=" N ARG I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 120 Processing helix chain 'I' and resid 121 through 133 Processing helix chain 'I' and resid 169 through 181 Processing helix chain 'J' and resid 49 through 51 No H-bonds generated for 'chain 'J' and resid 49 through 51' Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.909A pdb=" N VAL J 91 " --> pdb=" O ASN J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 118 Processing helix chain 'J' and resid 134 through 139 Processing helix chain 'J' and resid 142 through 154 Processing helix chain 'J' and resid 159 through 169 Processing helix chain 'J' and resid 178 through 183 Processing helix chain 'J' and resid 192 through 207 removed outlier: 3.510A pdb=" N GLU J 196 " --> pdb=" O GLY J 192 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY J 207 " --> pdb=" O LYS J 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 36 Processing helix chain 'K' and resid 39 through 63 removed outlier: 4.367A pdb=" N VAL K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 84 Processing helix chain 'K' and resid 101 through 107 removed outlier: 4.083A pdb=" N PHE K 105 " --> pdb=" O LYS K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 117 Processing helix chain 'K' and resid 122 through 132 Processing helix chain 'K' and resid 153 through 155 No H-bonds generated for 'chain 'K' and resid 153 through 155' Processing helix chain 'K' and resid 171 through 185 Processing helix chain 'L' and resid 4 through 18 removed outlier: 3.697A pdb=" N ARG L 8 " --> pdb=" O PRO L 4 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU L 18 " --> pdb=" O LEU L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 56 removed outlier: 4.217A pdb=" N VAL L 45 " --> pdb=" O PRO L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 84 Processing helix chain 'M' and resid 48 through 53 Processing helix chain 'N' and resid 15 through 28 Processing helix chain 'N' and resid 35 through 44 Processing helix chain 'N' and resid 60 through 70 Processing helix chain 'N' and resid 81 through 90 removed outlier: 3.778A pdb=" N LEU N 85 " --> pdb=" O ASP N 81 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL N 89 " --> pdb=" O LEU N 85 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY N 90 " --> pdb=" O GLY N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 119 through 129 Processing helix chain 'O' and resid 29 through 44 Processing helix chain 'O' and resid 46 through 58 Processing helix chain 'O' and resid 70 through 79 Processing helix chain 'O' and resid 85 through 103 Processing helix chain 'O' and resid 108 through 132 Processing helix chain 'O' and resid 142 through 149 removed outlier: 3.646A pdb=" N SER O 147 " --> pdb=" O SER O 143 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA O 148 " --> pdb=" O SER O 144 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 61 No H-bonds generated for 'chain 'P' and resid 59 through 61' Processing helix chain 'P' and resid 70 through 89 Processing helix chain 'P' and resid 111 through 122 Processing helix chain 'Q' and resid 21 through 27 Processing helix chain 'Q' and resid 29 through 37 removed outlier: 4.328A pdb=" N GLN Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 46 Processing helix chain 'Q' and resid 54 through 66 Processing helix chain 'Q' and resid 115 through 120 removed outlier: 4.303A pdb=" N PHE Q 119 " --> pdb=" O TYR Q 115 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER Q 120 " --> pdb=" O LEU Q 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 115 through 120' Processing helix chain 'R' and resid 38 through 42 removed outlier: 3.722A pdb=" N ILE R 42 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 46 No H-bonds generated for 'chain 'R' and resid 44 through 46' Processing helix chain 'R' and resid 47 through 52 Processing helix chain 'R' and resid 52 through 59 Processing helix chain 'R' and resid 77 through 100 removed outlier: 4.064A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 3.895A pdb=" N LYS R 105 " --> pdb=" O ASP R 101 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE R 111 " --> pdb=" O GLU R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 120 removed outlier: 3.596A pdb=" N LEU R 120 " --> pdb=" O ARG R 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 117 through 120' Processing helix chain 'S' and resid 6 through 20 Processing helix chain 'S' and resid 27 through 38 Processing helix chain 'S' and resid 44 through 64 Processing helix chain 'S' and resid 76 through 82 Processing helix chain 'S' and resid 99 through 108 Processing helix chain 'T' and resid 25 through 30 removed outlier: 4.405A pdb=" N ILE T 30 " --> pdb=" O ILE T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 33 No H-bonds generated for 'chain 'T' and resid 31 through 33' Processing helix chain 'T' and resid 38 through 45 removed outlier: 3.569A pdb=" N VAL T 43 " --> pdb=" O ARG T 39 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 73 Processing helix chain 'T' and resid 74 through 78 removed outlier: 3.621A pdb=" N TYR T 77 " --> pdb=" O PRO T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 118 Processing helix chain 'T' and resid 119 through 128 Processing helix chain 'U' and resid 10 through 26 removed outlier: 3.645A pdb=" N PHE U 14 " --> pdb=" O ASN U 10 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG U 16 " --> pdb=" O GLN U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 35 removed outlier: 3.838A pdb=" N VAL U 34 " --> pdb=" O PRO U 31 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP U 35 " --> pdb=" O GLU U 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 31 through 35' Processing helix chain 'U' and resid 51 through 67 removed outlier: 3.969A pdb=" N THR U 55 " --> pdb=" O ASN U 51 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 79 Processing helix chain 'U' and resid 97 through 110 Processing helix chain 'U' and resid 124 through 143 Processing helix chain 'V' and resid 28 through 46 Processing helix chain 'V' and resid 94 through 103 removed outlier: 3.663A pdb=" N VAL V 98 " --> pdb=" O PRO V 94 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 63 Processing helix chain 'W' and resid 65 through 77 Processing helix chain 'X' and resid 6 through 21 Processing helix chain 'X' and resid 31 through 45 Processing helix chain 'X' and resid 85 through 94 removed outlier: 3.926A pdb=" N TRP X 89 " --> pdb=" O ASP X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 112 through 119 Processing helix chain 'Y' and resid 10 through 23 Processing helix chain 'Y' and resid 25 through 31 Processing helix chain 'Y' and resid 32 through 38 removed outlier: 3.651A pdb=" N LEU Y 36 " --> pdb=" O LEU Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 135 Processing helix chain 'Z' and resid 36 through 49 removed outlier: 3.861A pdb=" N ILE Z 40 " --> pdb=" O PRO Z 36 " (cutoff:3.500A) Processing helix chain 'Z' and resid 78 through 85 Processing helix chain 'Z' and resid 87 through 94 removed outlier: 4.042A pdb=" N LEU Z 91 " --> pdb=" O PRO Z 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 117 removed outlier: 3.733A pdb=" N VAL Z 117 " --> pdb=" O ARG Z 113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 118 through 120 No H-bonds generated for 'chain 'Z' and resid 118 through 120' Processing helix chain 'Z' and resid 121 through 126 removed outlier: 3.693A pdb=" N GLY Z 126 " --> pdb=" O LYS Z 122 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 62 Processing helix chain 'a' and resid 69 through 78 Processing helix chain 'a' and resid 80 through 95 Processing helix chain 'b' and resid 49 through 56 Processing helix chain 'b' and resid 74 through 81 Processing helix chain 'c' and resid 11 through 18 removed outlier: 3.601A pdb=" N LYS c 18 " --> pdb=" O GLU c 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 3 through 7 Processing helix chain 'e' and resid 32 through 36 removed outlier: 3.614A pdb=" N LEU e 36 " --> pdb=" O LYS e 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 39 through 46 Processing helix chain 'e' and resid 46 through 51 removed outlier: 3.615A pdb=" N ILE e 50 " --> pdb=" O TYR e 46 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY e 51 " --> pdb=" O ALA e 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 46 through 51' Processing helix chain 'f' and resid 83 through 88 Processing helix chain 'f' and resid 104 through 116 Processing helix chain 'g' and resid 101 through 104 Processing helix chain 'n' and resid 2 through 24 removed outlier: 3.690A pdb=" N ARG n 6 " --> pdb=" O ARG n 2 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 38 through 41 removed outlier: 7.161A pdb=" N ILE B 48 " --> pdb=" O TYR B 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.384A pdb=" N SER B 75 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA B 146 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 50 removed outlier: 4.844A pdb=" N GLY C 45 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL C 33 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N CYS C 96 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASP C 32 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N THR C 98 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LYS C 34 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N PHE C 100 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU C 97 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU C 89 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS C 85 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N MET C 103 " --> pdb=" O LYS C 83 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LYS C 83 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG C 65 " --> pdb=" O THR C 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 50 removed outlier: 4.844A pdb=" N GLY C 45 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL C 33 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N CYS C 96 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASP C 32 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N THR C 98 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LYS C 34 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N PHE C 100 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N HIS C 101 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET C 217 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ARG C 213 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL C 210 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N PHE C 142 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL C 212 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL C 140 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS C 214 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 137 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL C 125 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 104 through 115 removed outlier: 5.900A pdb=" N VAL D 106 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS D 108 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS D 125 " --> pdb=" O MET D 110 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS D 142 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL D 128 " --> pdb=" O GLY D 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 184 through 188 removed outlier: 3.502A pdb=" N VAL D 193 " --> pdb=" O GLY D 186 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS D 188 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU D 192 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG D 227 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL D 205 " --> pdb=" O CYS D 222 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR D 224 " --> pdb=" O VAL D 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 34 through 42 removed outlier: 7.137A pdb=" N LEU E 51 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N VAL E 37 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ILE E 49 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL E 39 " --> pdb=" O GLU E 47 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N GLU E 47 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL E 41 " --> pdb=" O ARG E 45 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ARG E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 147 through 155 removed outlier: 3.790A pdb=" N VAL E 136 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LYS E 141 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL E 181 " --> pdb=" O LYS E 141 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA E 171 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 209 through 210 removed outlier: 4.101A pdb=" N SER E 209 " --> pdb=" O ILE S 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 224 through 226 removed outlier: 3.630A pdb=" N GLU E 225 " --> pdb=" O ASN h 187 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN h 187 " --> pdb=" O GLU E 225 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL h 176 " --> pdb=" O LYS h 185 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASN h 187 " --> pdb=" O VAL h 174 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL h 174 " --> pdb=" O ASN h 187 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 9 through 10 removed outlier: 4.482A pdb=" N LEU F 9 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AB4, first strand: chain 'F' and resid 75 through 76 removed outlier: 4.121A pdb=" N ASN F 98 " --> pdb=" O ILE F 114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 102 through 103 removed outlier: 4.428A pdb=" N ILE F 102 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.666A pdb=" N VAL F 140 " --> pdb=" O LYS F 128 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS F 128 " --> pdb=" O VAL F 140 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR F 159 " --> pdb=" O ILE F 173 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP F 171 " --> pdb=" O GLN F 161 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP F 163 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE F 169 " --> pdb=" O ASP F 163 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 217 through 221 removed outlier: 3.544A pdb=" N THR F 220 " --> pdb=" O VAL F 208 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL F 207 " --> pdb=" O ARG F 198 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ARG F 198 " --> pdb=" O VAL F 207 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N HIS F 209 " --> pdb=" O THR F 196 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU F 180 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE F 228 " --> pdb=" O LEU F 180 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS F 230 " --> pdb=" O LYS F 233 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 123 through 127 removed outlier: 18.826A pdb=" N ARG G 136 " --> pdb=" O ILE d 43 " (cutoff:3.500A) removed outlier: 13.810A pdb=" N ASN d 45 " --> pdb=" O ARG G 136 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N ALA G 138 " --> pdb=" O ASN d 45 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LYS d 47 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASP G 140 " --> pdb=" O LYS d 47 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLN d 29 " --> pdb=" O VAL d 17 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N VAL d 17 " --> pdb=" O GLN d 29 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG d 31 " --> pdb=" O THR d 15 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 13 through 17 removed outlier: 6.954A pdb=" N ASN H 56 " --> pdb=" O SER H 107 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N LEU H 109 " --> pdb=" O GLY H 54 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N GLY H 54 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU H 111 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE H 52 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE H 113 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL H 50 " --> pdb=" O ILE H 113 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL H 36 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 72 through 77 Processing sheet with id=AC2, first strand: chain 'H' and resid 160 through 162 removed outlier: 3.799A pdb=" N ARG H 170 " --> pdb=" O LEU H 162 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 48 through 50 Processing sheet with id=AC4, first strand: chain 'I' and resid 185 through 188 removed outlier: 3.720A pdb=" N LEU I 158 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS I 142 " --> pdb=" O ASP X 54 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP X 54 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE X 52 " --> pdb=" O ILE I 144 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL I 146 " --> pdb=" O PHE X 50 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE X 50 " --> pdb=" O VAL I 146 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 42 through 47 removed outlier: 7.034A pdb=" N ARG J 42 " --> pdb=" O LEU J 58 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL J 46 " --> pdb=" O LYS J 54 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 62 through 67 removed outlier: 3.659A pdb=" N CYS J 72 " --> pdb=" O TRP J 67 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE J 101 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N CYS J 100 " --> pdb=" O ILE J 175 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY J 187 " --> pdb=" O ASN J 64 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 141 through 142 removed outlier: 4.684A pdb=" N ILE K 135 " --> pdb=" O VAL K 142 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP K 158 " --> pdb=" O ARG K 136 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 20 through 24 removed outlier: 4.021A pdb=" N MET L 21 " --> pdb=" O TRP L 69 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP L 69 " --> pdb=" O MET L 21 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA L 23 " --> pdb=" O PHE L 67 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 72 through 79 removed outlier: 7.240A pdb=" N VAL M 87 " --> pdb=" O THR M 78 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N SER M 110 " --> pdb=" O VAL M 138 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE M 140 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N THR M 127 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL M 145 " --> pdb=" O ILE M 125 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE M 125 " --> pdb=" O VAL M 145 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 91 through 96 removed outlier: 3.645A pdb=" N TYR M 92 " --> pdb=" O ARG M 105 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE M 96 " --> pdb=" O ARG M 101 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG M 101 " --> pdb=" O ILE M 96 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 31 through 33 removed outlier: 4.085A pdb=" N LEU N 49 " --> pdb=" O VAL N 111 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 52 through 57 removed outlier: 4.240A pdb=" N CYS P 54 " --> pdb=" O VAL P 44 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL P 56 " --> pdb=" O VAL P 42 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL P 42 " --> pdb=" O VAL P 56 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL P 30 " --> pdb=" O THR P 45 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU P 93 " --> pdb=" O ILE P 126 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ARG P 128 " --> pdb=" O LEU P 93 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 76 through 78 removed outlier: 5.863A pdb=" N VAL Q 76 " --> pdb=" O GLY Q 95 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N TYR Q 97 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N THR Q 78 " --> pdb=" O TYR Q 97 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL Q 94 " --> pdb=" O VAL Q 105 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL Q 105 " --> pdb=" O VAL Q 94 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL Q 96 " --> pdb=" O ASN Q 103 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 10 through 12 removed outlier: 3.507A pdb=" N LYS R 26 " --> pdb=" O ASP R 67 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU R 31 " --> pdb=" O VAL R 66 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 96 through 98 Processing sheet with id=AD7, first strand: chain 'T' and resid 12 through 15 removed outlier: 3.946A pdb=" N VAL T 15 " --> pdb=" O THR T 18 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'U' and resid 81 through 83 Processing sheet with id=AD9, first strand: chain 'V' and resid 54 through 55 removed outlier: 3.841A pdb=" N ILE V 84 " --> pdb=" O LYS V 59 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS V 59 " --> pdb=" O ILE V 84 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'V' and resid 54 through 55 removed outlier: 3.915A pdb=" N HIS V 85 " --> pdb=" O SER V 26 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER V 26 " --> pdb=" O HIS V 85 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU V 91 " --> pdb=" O ILE V 20 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE V 20 " --> pdb=" O LEU V 91 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR V 115 " --> pdb=" O ARG V 21 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU V 113 " --> pdb=" O THR V 23 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'V' and resid 63 through 66 Processing sheet with id=AE3, first strand: chain 'W' and resid 32 through 39 removed outlier: 4.878A pdb=" N GLN W 49 " --> pdb=" O GLU W 38 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'X' and resid 24 through 27 Processing sheet with id=AE5, first strand: chain 'X' and resid 71 through 74 removed outlier: 3.769A pdb=" N LYS X 71 " --> pdb=" O PHE X 130 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE X 130 " --> pdb=" O LYS X 71 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY X 123 " --> pdb=" O VAL X 81 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'X' and resid 71 through 74 removed outlier: 3.769A pdb=" N LYS X 71 " --> pdb=" O PHE X 130 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE X 130 " --> pdb=" O LYS X 71 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE X 125 " --> pdb=" O THR X 105 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N THR X 105 " --> pdb=" O ILE X 125 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET X 111 " --> pdb=" O LEU X 104 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Y' and resid 128 through 129 removed outlier: 5.482A pdb=" N VAL Y 122 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA Y 103 " --> pdb=" O VAL Y 122 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL Y 51 " --> pdb=" O GLN Y 73 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLN Y 73 " --> pdb=" O VAL Y 51 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU Y 53 " --> pdb=" O ARG Y 71 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N PHE Y 120 " --> pdb=" O LYS Y 80 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR Y 82 " --> pdb=" O PHE Y 120 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL Y 122 " --> pdb=" O THR Y 82 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE Y 84 " --> pdb=" O VAL Y 122 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N LYS Y 124 " --> pdb=" O PHE Y 84 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Z' and resid 6 through 15 removed outlier: 4.338A pdb=" N PHE Z 12 " --> pdb=" O GLN Z 22 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLN Z 22 " --> pdb=" O PHE Z 12 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N THR Z 14 " --> pdb=" O ARG Z 20 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG Z 20 " --> pdb=" O THR Z 14 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL Z 27 " --> pdb=" O THR Z 69 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR Z 69 " --> pdb=" O VAL Z 27 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR Z 70 " --> pdb=" O PHE Z 60 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE Z 60 " --> pdb=" O THR Z 70 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE Z 58 " --> pdb=" O PHE Z 72 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'b' and resid 20 through 22 Processing sheet with id=AF1, first strand: chain 'b' and resid 36 through 43 removed outlier: 3.551A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'c' and resid 44 through 47 removed outlier: 4.120A pdb=" N ASP c 34 " --> pdb=" O ARG c 80 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG c 80 " --> pdb=" O ASP c 34 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER c 78 " --> pdb=" O LYS c 36 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'g' and resid 106 through 108 Processing sheet with id=AF4, first strand: chain 'h' and resid 5 through 6 Processing sheet with id=AF5, first strand: chain 'h' and resid 10 through 11 removed outlier: 4.073A pdb=" N ARG h 308 " --> pdb=" O ALA h 300 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA h 300 " --> pdb=" O ARG h 308 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N PHE h 299 " --> pdb=" O LEU h 289 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU h 289 " --> pdb=" O PHE h 299 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLY h 301 " --> pdb=" O THR h 287 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'h' and resid 18 through 22 removed outlier: 3.685A pdb=" N GLN h 20 " --> pdb=" O ALA h 34 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU h 32 " --> pdb=" O ALA h 22 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE h 31 " --> pdb=" O TRP h 43 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER h 33 " --> pdb=" O ILE h 41 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE h 41 " --> pdb=" O SER h 33 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE h 40 " --> pdb=" O ALA h 58 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA h 58 " --> pdb=" O ILE h 40 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N MET h 42 " --> pdb=" O GLN h 56 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'h' and resid 66 through 71 removed outlier: 6.834A pdb=" N GLY h 81 " --> pdb=" O SER h 67 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL h 69 " --> pdb=" O LEU h 79 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU h 79 " --> pdb=" O VAL h 69 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ILE h 71 " --> pdb=" O PHE h 77 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE h 77 " --> pdb=" O ILE h 71 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU h 87 " --> pdb=" O ARG h 100 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG h 100 " --> pdb=" O LEU h 87 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU h 89 " --> pdb=" O THR h 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'h' and resid 108 through 113 removed outlier: 6.505A pdb=" N GLY h 123 " --> pdb=" O LEU h 109 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL h 111 " --> pdb=" O VAL h 121 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL h 121 " --> pdb=" O VAL h 111 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE h 120 " --> pdb=" O TRP h 132 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR h 140 " --> pdb=" O LEU h 131 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'h' and resid 195 through 200 removed outlier: 3.951A pdb=" N THR h 197 " --> pdb=" O GLY h 210 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY h 210 " --> pdb=" O THR h 197 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR h 199 " --> pdb=" O ALA h 208 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLY h 211 " --> pdb=" O GLN h 215 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLN h 215 " --> pdb=" O GLY h 211 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU h 230 " --> pdb=" O ALA h 216 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'h' and resid 238 through 241 removed outlier: 3.906A pdb=" N ALA h 238 " --> pdb=" O ALA h 251 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU h 248 " --> pdb=" O TRP h 259 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE h 258 " --> pdb=" O ASP h 268 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASP h 268 " --> pdb=" O ILE h 258 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP h 260 " --> pdb=" O ILE h 266 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE h 266 " --> pdb=" O ASP h 260 " (cutoff:3.500A) 1406 hydrogen bonds defined for protein. 4068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1317 hydrogen bonds 2192 hydrogen bond angles 0 basepair planarities 522 basepair parallelities 1042 stacking parallelities Total time for adding SS restraints: 61.03 Time building geometry restraints manager: 30.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 14153 1.33 - 1.45: 31737 1.45 - 1.58: 36497 1.58 - 1.70: 3905 1.70 - 1.82: 274 Bond restraints: 86566 Sorted by residual: bond pdb=" C PHE I 135 " pdb=" N PRO I 136 " ideal model delta sigma weight residual 1.337 1.387 -0.050 9.80e-03 1.04e+04 2.60e+01 bond pdb=" C VAL S 98 " pdb=" N ASP S 99 " ideal model delta sigma weight residual 1.330 1.394 -0.064 1.47e-02 4.63e+03 1.92e+01 bond pdb=" C ARG X 28 " pdb=" N PRO X 29 " ideal model delta sigma weight residual 1.328 1.372 -0.044 1.25e-02 6.40e+03 1.24e+01 bond pdb=" C ASP E 162 " pdb=" N PRO E 163 " ideal model delta sigma weight residual 1.334 1.405 -0.071 2.34e-02 1.83e+03 9.18e+00 bond pdb=" CA GLN E 4 " pdb=" CB GLN E 4 " ideal model delta sigma weight residual 1.532 1.563 -0.031 1.36e-02 5.41e+03 5.30e+00 ... (remaining 86561 not shown) Histogram of bond angle deviations from ideal: 98.10 - 105.85: 10890 105.85 - 113.60: 51854 113.60 - 121.36: 41035 121.36 - 129.11: 20982 129.11 - 136.86: 1514 Bond angle restraints: 126275 Sorted by residual: angle pdb=" CA GLN E 4 " pdb=" CB GLN E 4 " pdb=" CG GLN E 4 " ideal model delta sigma weight residual 114.10 127.75 -13.65 2.00e+00 2.50e-01 4.66e+01 angle pdb=" C VAL G 141 " pdb=" N SER G 142 " pdb=" CA SER G 142 " ideal model delta sigma weight residual 120.68 130.10 -9.42 1.52e+00 4.33e-01 3.84e+01 angle pdb=" C GLU S 75 " pdb=" N GLU S 76 " pdb=" CA GLU S 76 " ideal model delta sigma weight residual 121.54 132.40 -10.86 1.91e+00 2.74e-01 3.23e+01 angle pdb=" CB LYS Q 64 " pdb=" CG LYS Q 64 " pdb=" CD LYS Q 64 " ideal model delta sigma weight residual 111.30 123.84 -12.54 2.30e+00 1.89e-01 2.97e+01 angle pdb=" C GLY M 150 " pdb=" N THR M 151 " pdb=" CA THR M 151 " ideal model delta sigma weight residual 122.46 130.14 -7.68 1.41e+00 5.03e-01 2.96e+01 ... (remaining 126270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 46496 35.98 - 71.95: 1474 71.95 - 107.93: 117 107.93 - 143.91: 15 143.91 - 179.88: 28 Dihedral angle restraints: 48130 sinusoidal: 34057 harmonic: 14073 Sorted by residual: dihedral pdb=" O4' C 21303 " pdb=" C1' C 21303 " pdb=" N1 C 21303 " pdb=" C2 C 21303 " ideal model delta sinusoidal sigma weight residual 200.00 26.85 173.15 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' C 21139 " pdb=" C1' C 21139 " pdb=" N1 C 21139 " pdb=" C2 C 21139 " ideal model delta sinusoidal sigma weight residual -160.00 3.46 -163.46 1 1.50e+01 4.44e-03 8.36e+01 dihedral pdb=" O4' C 21057 " pdb=" C1' C 21057 " pdb=" N1 C 21057 " pdb=" C2 C 21057 " ideal model delta sinusoidal sigma weight residual 200.00 42.47 157.53 1 1.50e+01 4.44e-03 8.21e+01 ... (remaining 48127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 14864 0.089 - 0.178: 777 0.178 - 0.267: 49 0.267 - 0.356: 11 0.356 - 0.445: 2 Chirality restraints: 15703 Sorted by residual: chirality pdb=" CB ILE Z 55 " pdb=" CA ILE Z 55 " pdb=" CG1 ILE Z 55 " pdb=" CG2 ILE Z 55 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.95e+00 chirality pdb=" CB ILE Q 85 " pdb=" CA ILE Q 85 " pdb=" CG1 ILE Q 85 " pdb=" CG2 ILE Q 85 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CB ILE P 135 " pdb=" CA ILE P 135 " pdb=" CG1 ILE P 135 " pdb=" CG2 ILE P 135 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 15700 not shown) Planarity restraints: 8745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 90 " 0.095 5.00e-02 4.00e+02 1.41e-01 3.19e+01 pdb=" N PRO L 91 " -0.244 5.00e-02 4.00e+02 pdb=" CA PRO L 91 " 0.076 5.00e-02 4.00e+02 pdb=" CD PRO L 91 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 42 " -0.067 5.00e-02 4.00e+02 1.02e-01 1.65e+01 pdb=" N PRO F 43 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO F 43 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO F 43 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU O 35 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" CD GLU O 35 " 0.056 2.00e-02 2.50e+03 pdb=" OE1 GLU O 35 " -0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU O 35 " -0.020 2.00e-02 2.50e+03 ... (remaining 8742 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 15755 2.78 - 3.31: 65580 3.31 - 3.84: 154065 3.84 - 4.37: 177707 4.37 - 4.90: 260286 Nonbonded interactions: 673393 Sorted by model distance: nonbonded pdb=" O TYR I 177 " pdb=" OG1 THR I 181 " model vdw 2.251 2.440 nonbonded pdb=" O ASN E 22 " pdb=" OG1 THR E 26 " model vdw 2.272 2.440 nonbonded pdb=" O2' U 2 918 " pdb=" O4' A 2 919 " model vdw 2.280 2.440 nonbonded pdb=" O2' U 21201 " pdb=" O2' U 21358 " model vdw 2.285 2.440 nonbonded pdb=" OP1 G 21345 " pdb=" O2' C 21688 " model vdw 2.285 2.440 ... (remaining 673388 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1958 5.49 5 S 180 5.16 5 C 43389 2.51 5 N 14905 2.21 5 O 20529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 18.340 Check model and map are aligned: 0.890 Convert atoms to be neutral: 0.530 Process input model: 211.510 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 240.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.087 86566 Z= 0.207 Angle : 0.796 13.992 126275 Z= 0.394 Chirality : 0.041 0.445 15703 Planarity : 0.007 0.141 8745 Dihedral : 15.146 179.882 39051 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.10), residues: 4827 helix: -1.64 (0.11), residues: 1500 sheet: -1.03 (0.19), residues: 684 loop : -2.06 (0.10), residues: 2643 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 751 time to evaluate : 4.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 753 average time/residue: 0.7584 time to fit residues: 982.8275 Evaluate side-chains 560 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 559 time to evaluate : 4.641 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5768 time to fit residues: 6.8210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 669 random chunks: chunk 564 optimal weight: 7.9990 chunk 507 optimal weight: 6.9990 chunk 281 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 chunk 342 optimal weight: 8.9990 chunk 270 optimal weight: 0.0370 chunk 524 optimal weight: 9.9990 chunk 202 optimal weight: 10.0000 chunk 318 optimal weight: 0.0010 chunk 390 optimal weight: 20.0000 chunk 607 optimal weight: 0.0060 overall best weight: 2.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 43 ASN E 101 GLN F 161 GLN G 83 ASN ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN H 65 GLN J 64 ASN J 138 ASN L 50 GLN M 11 GLN P 94 HIS Q 104 GLN S 127 ASN U 126 GLN X 90 GLN ** Z 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 110 GLN h 191 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 86566 Z= 0.144 Angle : 0.532 10.780 126275 Z= 0.270 Chirality : 0.034 0.227 15703 Planarity : 0.005 0.094 8745 Dihedral : 14.764 179.216 28924 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.11), residues: 4827 helix: -0.23 (0.13), residues: 1523 sheet: -0.93 (0.18), residues: 762 loop : -1.83 (0.11), residues: 2542 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 697 time to evaluate : 4.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 700 average time/residue: 0.7319 time to fit residues: 894.5558 Evaluate side-chains 543 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 542 time to evaluate : 4.580 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6636 time to fit residues: 6.8036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 669 random chunks: chunk 337 optimal weight: 20.0000 chunk 188 optimal weight: 4.9990 chunk 505 optimal weight: 10.0000 chunk 413 optimal weight: 9.9990 chunk 167 optimal weight: 20.0000 chunk 608 optimal weight: 30.0000 chunk 657 optimal weight: 30.0000 chunk 542 optimal weight: 20.0000 chunk 603 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 488 optimal weight: 10.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN C 43 ASN C 95 ASN D 113 GLN F 161 GLN F 179 ASN ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 GLN H 65 GLN H 186 GLN ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 162 GLN Q 54 HIS R 24 HIS T 11 HIS X 56 HIS ** Y 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 65 GLN d 29 GLN f 88 GLN ** f 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 191 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 86566 Z= 0.295 Angle : 0.666 9.997 126275 Z= 0.335 Chirality : 0.039 0.252 15703 Planarity : 0.006 0.078 8745 Dihedral : 15.281 179.600 28924 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.11), residues: 4827 helix: 0.14 (0.13), residues: 1529 sheet: -1.22 (0.17), residues: 805 loop : -1.85 (0.11), residues: 2493 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 636 time to evaluate : 4.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 641 average time/residue: 0.7293 time to fit residues: 809.4067 Evaluate side-chains 501 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 500 time to evaluate : 4.538 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5586 time to fit residues: 6.5511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 669 random chunks: chunk 601 optimal weight: 4.9990 chunk 457 optimal weight: 2.9990 chunk 315 optimal weight: 0.6980 chunk 67 optimal weight: 10.0000 chunk 290 optimal weight: 10.0000 chunk 408 optimal weight: 3.9990 chunk 610 optimal weight: 20.0000 chunk 646 optimal weight: 40.0000 chunk 319 optimal weight: 5.9990 chunk 578 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN C 95 ASN F 161 GLN F 179 ASN ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 ASN K 27 GLN Q 54 HIS T 11 HIS U 126 GLN Z 15 ASN ** a 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 65 GLN d 29 GLN e 16 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 86566 Z= 0.157 Angle : 0.540 10.219 126275 Z= 0.275 Chirality : 0.035 0.238 15703 Planarity : 0.005 0.070 8745 Dihedral : 15.099 179.822 28924 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.12), residues: 4827 helix: 0.60 (0.13), residues: 1535 sheet: -1.12 (0.17), residues: 793 loop : -1.77 (0.12), residues: 2499 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 674 time to evaluate : 6.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 679 average time/residue: 0.7511 time to fit residues: 877.3160 Evaluate side-chains 522 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 521 time to evaluate : 4.539 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6514 time to fit residues: 6.5938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 669 random chunks: chunk 538 optimal weight: 20.0000 chunk 367 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 481 optimal weight: 20.0000 chunk 266 optimal weight: 7.9990 chunk 551 optimal weight: 0.0370 chunk 446 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 330 optimal weight: 2.9990 chunk 580 optimal weight: 9.9990 chunk 163 optimal weight: 30.0000 overall best weight: 6.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN C 95 ASN C 177 GLN D 113 GLN E 174 HIS F 161 GLN F 179 ASN ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN K 75 ASN Q 54 HIS U 63 HIS Y 46 HIS Z 15 ASN c 65 GLN d 29 GLN e 16 GLN f 88 GLN ** h 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.100 86566 Z= 0.252 Angle : 0.643 15.893 126275 Z= 0.325 Chirality : 0.038 0.258 15703 Planarity : 0.006 0.074 8745 Dihedral : 15.425 178.813 28924 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.12), residues: 4827 helix: 0.43 (0.13), residues: 1542 sheet: -1.29 (0.17), residues: 805 loop : -1.87 (0.11), residues: 2480 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 652 time to evaluate : 4.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 658 average time/residue: 0.7482 time to fit residues: 847.1903 Evaluate side-chains 508 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 505 time to evaluate : 4.538 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5873 time to fit residues: 8.7883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 669 random chunks: chunk 217 optimal weight: 7.9990 chunk 582 optimal weight: 6.9990 chunk 127 optimal weight: 30.0000 chunk 379 optimal weight: 10.0000 chunk 159 optimal weight: 30.0000 chunk 647 optimal weight: 40.0000 chunk 537 optimal weight: 9.9990 chunk 299 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 chunk 339 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN E 174 HIS F 161 GLN ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN H 187 HIS ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 163 GLN ** J 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN K 124 HIS ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN T 11 HIS U 83 GLN U 126 GLN c 65 GLN d 29 GLN f 88 GLN ** h 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 86566 Z= 0.271 Angle : 0.672 12.927 126275 Z= 0.340 Chirality : 0.040 0.324 15703 Planarity : 0.006 0.081 8745 Dihedral : 15.671 179.293 28924 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.11), residues: 4827 helix: 0.30 (0.13), residues: 1532 sheet: -1.28 (0.17), residues: 804 loop : -1.94 (0.12), residues: 2491 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 639 time to evaluate : 4.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 641 average time/residue: 0.7463 time to fit residues: 826.4785 Evaluate side-chains 494 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 493 time to evaluate : 4.587 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6713 time to fit residues: 6.6748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 669 random chunks: chunk 624 optimal weight: 4.9990 chunk 72 optimal weight: 30.0000 chunk 368 optimal weight: 0.9990 chunk 472 optimal weight: 7.9990 chunk 366 optimal weight: 7.9990 chunk 544 optimal weight: 9.9990 chunk 361 optimal weight: 8.9990 chunk 644 optimal weight: 30.0000 chunk 403 optimal weight: 6.9990 chunk 393 optimal weight: 0.9990 chunk 297 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN D 113 GLN E 174 HIS F 161 GLN ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 165 GLN K 27 GLN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 54 HIS ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 35 ASN ** X 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 15 ASN c 65 GLN d 29 GLN e 3 HIS e 16 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 86566 Z= 0.181 Angle : 0.586 14.200 126275 Z= 0.298 Chirality : 0.037 0.246 15703 Planarity : 0.005 0.075 8745 Dihedral : 15.502 179.443 28924 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.12), residues: 4827 helix: 0.55 (0.13), residues: 1536 sheet: -1.18 (0.17), residues: 813 loop : -1.87 (0.12), residues: 2478 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 658 time to evaluate : 4.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 662 average time/residue: 0.7643 time to fit residues: 870.7927 Evaluate side-chains 507 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 507 time to evaluate : 4.612 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 669 random chunks: chunk 398 optimal weight: 9.9990 chunk 257 optimal weight: 10.0000 chunk 385 optimal weight: 9.9990 chunk 194 optimal weight: 0.0370 chunk 126 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 409 optimal weight: 20.0000 chunk 439 optimal weight: 9.9990 chunk 318 optimal weight: 5.9990 chunk 60 optimal weight: 20.0000 chunk 506 optimal weight: 7.9990 overall best weight: 6.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN D 115 GLN E 174 HIS F 161 GLN ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 157 HIS I 163 GLN J 165 GLN K 27 GLN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 126 GLN Z 15 ASN d 29 GLN e 16 GLN ** f 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 222 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 86566 Z= 0.265 Angle : 0.666 15.387 126275 Z= 0.337 Chirality : 0.040 0.256 15703 Planarity : 0.006 0.099 8745 Dihedral : 15.722 179.415 28924 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.46 % Favored : 92.52 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.12), residues: 4827 helix: 0.39 (0.13), residues: 1528 sheet: -1.27 (0.18), residues: 801 loop : -1.94 (0.12), residues: 2498 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 633 time to evaluate : 4.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 637 average time/residue: 0.7450 time to fit residues: 820.3245 Evaluate side-chains 492 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 490 time to evaluate : 4.619 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.6669 time to fit residues: 7.9604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 669 random chunks: chunk 586 optimal weight: 0.3980 chunk 617 optimal weight: 8.9990 chunk 563 optimal weight: 9.9990 chunk 600 optimal weight: 0.0370 chunk 361 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 471 optimal weight: 2.9990 chunk 184 optimal weight: 0.7980 chunk 542 optimal weight: 0.0670 chunk 568 optimal weight: 20.0000 chunk 598 optimal weight: 8.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN C 43 ASN ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 HIS E 174 HIS F 161 GLN ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 165 GLN K 27 GLN M 108 ASN Q 54 HIS ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 126 GLN Z 15 ASN b 25 ASN d 29 GLN ** h 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.086 86566 Z= 0.133 Angle : 0.547 11.492 126275 Z= 0.278 Chirality : 0.034 0.230 15703 Planarity : 0.004 0.089 8745 Dihedral : 15.293 179.928 28924 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.12), residues: 4827 helix: 0.79 (0.13), residues: 1528 sheet: -1.00 (0.18), residues: 789 loop : -1.69 (0.12), residues: 2510 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 679 time to evaluate : 4.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 682 average time/residue: 0.7502 time to fit residues: 887.7559 Evaluate side-chains 511 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 511 time to evaluate : 4.546 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 669 random chunks: chunk 394 optimal weight: 20.0000 chunk 635 optimal weight: 7.9990 chunk 387 optimal weight: 4.9990 chunk 301 optimal weight: 1.9990 chunk 441 optimal weight: 20.0000 chunk 666 optimal weight: 30.0000 chunk 613 optimal weight: 7.9990 chunk 530 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 409 optimal weight: 0.8980 chunk 325 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN D 113 GLN E 174 HIS E 207 HIS F 161 GLN ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 165 GLN K 27 GLN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 GLN U 126 GLN Z 15 ASN b 25 ASN d 29 GLN f 88 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 86566 Z= 0.206 Angle : 0.596 13.829 126275 Z= 0.301 Chirality : 0.037 0.249 15703 Planarity : 0.005 0.090 8745 Dihedral : 15.427 179.633 28924 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.12), residues: 4827 helix: 0.70 (0.13), residues: 1532 sheet: -1.07 (0.18), residues: 803 loop : -1.74 (0.12), residues: 2492 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 633 time to evaluate : 4.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 636 average time/residue: 0.7182 time to fit residues: 795.9714 Evaluate side-chains 501 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 500 time to evaluate : 4.585 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6563 time to fit residues: 6.7014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 669 random chunks: chunk 421 optimal weight: 7.9990 chunk 565 optimal weight: 20.0000 chunk 162 optimal weight: 20.0000 chunk 489 optimal weight: 0.1980 chunk 78 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 531 optimal weight: 0.3980 chunk 222 optimal weight: 0.8980 chunk 545 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 overall best weight: 3.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN E 174 HIS F 161 GLN ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 165 GLN K 27 GLN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 54 HIS ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 90 GLN Z 15 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.062501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.048599 restraints weight = 572071.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.049968 restraints weight = 241533.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.050736 restraints weight = 140966.834| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 86566 Z= 0.158 Angle : 0.560 14.170 126275 Z= 0.284 Chirality : 0.035 0.239 15703 Planarity : 0.005 0.088 8745 Dihedral : 15.348 179.105 28924 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.12), residues: 4827 helix: 0.74 (0.13), residues: 1537 sheet: -1.01 (0.18), residues: 800 loop : -1.70 (0.12), residues: 2490 =============================================================================== Job complete usr+sys time: 13609.98 seconds wall clock time: 243 minutes 34.07 seconds (14614.07 seconds total)